Eukaryotic cells have genes not only in their nuclei but also in certain subcellular organelles. All eukaryotic cells have genes in nuclei and mitochondria; plant cells contain an additional set of different genes in their plastids. However, most of the proteins in organelles originate from nuclear genes. Some of these gene products interact with proteins encoded by organelle genes to form multimeric complexes such as energy transducing membranes, ribosomes, and multimeric enzymes. In fact, all multimeric components of organelles studied so far are mixtures of products of nuclear and organelle genes. Genetic diseases attributable to mutations in organelle genes as well as nuclear ones are known. The long range objective of this research program is to learn how organelle gene expression is regulated and integrated with the expression of nuclear genes. Such integration is essential for the proper development and differentiation of every eukaryotic cell from protists to higher animals and plants. The tools of molecular biology have permitted analysis of the structure of organelle chromosomes as well as the isolation, cloning and sequencing of organelle genes. Cloned genes have been used as templates for transcription by homologous RNA polymerases and modified cloned genes have been used to identify some sequences that control their transcription. The recent development of a method for the stable introduction of DNA into the plastid chromosome of the single celled organism Chlamydomonas reinhardtii now makes it possible to conveniently extend the results of transcription experiments in vitro to conditions in vivo. Furthermore, this transformation system opens the way to exploring mechanisms of integration of nuclear and organelle gene expression by altering the latter.